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PATENT WATCH: Jul 20, 2001

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Agilix Awarded Patent for ‘Universal Microarray’

New Haven, Conn. startup Agilix has gained the sole license to US Patent Number 6,261,782, which covers key technology in a microarray system that is designed to detect gene expression patterns in all genes from any organism. The patent, "Fixed address analysis of sequence tags," was awarded to Yale University July 12, and describes the FAAST transcription analysis system invented by Yale associate professor of pathology Paul Lizardi, a co-founder of Agilix.

Agilix is incorporating FAAST technology in its universal microarrays, which contain a probe set that can supposedly detect gene expression in any organism without the user having knowledge of the gene’s sequence. The FAAST system uses the same set of "universal probes" on each array. The advantage of this system, according to Agilix, is that these probes are not biased toward particular splice variants, and can be thoroughly characterized.

These microarrays have a universal sample chemistry as well, and have software for programming the probe addresses that is designed to handle up to one million addresses per experiment.

FAAST "puts us in the realm of a whole different paradigm," said Martin Mattessich, CEO of Agilix.

The probes are designed to look for gene expression in those genes that have not yet appeared on chips.

"There is far more sequence, or genes that have been sequenced than are on anyone’s chips," Mattessich said. "There’s a coverage gap that exists that is screaming for someone to fill."

Lizardi, who invented Rolling Circle Amplification and other DNA replication systems, developed FAAST in order to create a system that could look at what genes are active at the level of the transcriptome and proteome, Mattessich said.

The hardware consists of a simple microarray with a universal probe set, and the molecular biology generates a uniform and consistent sample chemistry. Software for programming these arrays can handle over a million transcript addresses per experiment.

Agilix is now offering the system under special early-access agreements. The price of individual arrays would be more than a single biochip, Mattessich said, but Agilix believes the quality of output will compensate for this cost.

Texas A&M, Affymetrix scientists Awarded BioMarker Patents for Breast, Colon Cancer

Texas A&M University has received US Patent Number 6,258,541 for isolating RNA from feces and using the RNA as a biomarker for colon cancer. The patent "Noninvasive detection of colonic biomarkers using fecal messenger RNA," describes a technique in which RNA is isolated from colonocytes in the fecal sample that were sloughed off during digestion. The inventors specified that the RNA biomarkers could be tested using a diagnostic microarray.

Affymetrix scientist Jonathan Oliner and several collaborators have been awarded US Patent number 6,258,536, "Expression monitoring of downstream genes in the BRCA1 pathway". The patent describes a set of genes whose expression is regulated by the BRCA1 gene, and details diagnostic applications for this set of genes. The genes can be used as biomarkers to determine whether a BRCA1 gene is mutated, the patent states. The patent also describes ways that the different alleles can be used to study the effects of different variants on BRCA1, as well as to diagnose neoplasia, and to aid in discovery of anti-neoplastic drugs.

Boston Biomedica Receives Patent for Novel Hybridization Technology

Boston Biomedica, of West Bridgewater, Mass., has been issued US Patent Number 6,258,534 for a method of controlling the specificity of nucleic acid hybridization in an optical cell. The patent, "Pressure controlled nucleic acid hybridization" describes the company’s Pressure Cycling Technology (PCT), which uses pressure to regulate hybridization. PCT works on the principle that high levels of pressure tend to stabilize perfect or near-perfect matches between oligonucleotide strands, and that pressurizing the reaction speeds up hybridization rates as well.

The company also said the technology can be used in the amplification of small amounts of DNA or RNA to replace the temperature cycling steps of PCR.

"This approach may be particularly well suited for detection of small changes in DNA sequences, such as those arising from mutations," said Mark Manak, senior vice president of R&D at Boston Biomedica, in a statement. "The technology may also be applicable to various screening applications, including new state-of-the-art biochip and array methods, in which the DNA from a single specimen can be simultaneously studied for numerous indications," Manak said.

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